Contacts of the strand formed by residues 170 - 176 (chain A) in PDB entry 3R4G
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A VAL* 3.8 5.9 - - - +
129A ASN* 5.1 1.3 + - - +
130A PHE* 5.9 0.6 - - - +
132A LEU* 3.6 54.0 + - + +
133A LYS 3.9 9.9 - - - +
134A HIS* 3.4 45.3 - - + +
139A VAL* 3.8 15.9 - - + -
140A LEU 3.6 11.7 - - - +
141A SER* 3.9 1.8 - - - +
168A HIS 3.4 1.4 + - - +
169A VAL* 1.3 80.4 - - - +
171A PHE* 1.3 65.0 + - - +
172A GLY 4.1 9.6 - - - +
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Residues in contact with PHE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LEU* 3.5 8.3 - - + +
67A LYS* 2.8 29.0 + - - -
71A VAL* 3.5 20.6 - - + -
74A THR* 3.7 20.4 - - + -
75A ALA* 4.5 5.6 - - - +
78A PHE* 3.4 44.9 - + + -
132A LEU* 4.5 1.1 - - - -
140A LEU* 2.9 37.4 + - + -
141A SER* 3.5 21.3 - - - -
142A MET* 3.4 31.0 - - + -
154A PHE* 4.3 1.8 - - + -
169A VAL 3.5 13.0 - - - -
170A VAL* 1.3 74.8 - - - +
172A GLY* 1.3 60.0 + - - +
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Residues in contact with GLY 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLU 3.0 14.4 - - - -
67A LYS* 4.3 10.0 - - - +
132A LEU* 4.9 0.4 - - - +
139A VAL* 3.9 2.8 - - - +
140A LEU* 3.0 33.3 + - - +
170A VAL* 3.9 8.6 - - - +
171A PHE* 1.3 79.8 - - - +
173A HIS* 1.3 67.8 + - - +
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Residues in contact with HIS 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 3.4 7.4 - - - -
65A GLU* 2.9 56.3 + - + -
67A LYS* 4.8 14.4 - - + -
138A GLY 3.2 16.4 - - - +
139A VAL* 4.5 4.3 - - + -
140A LEU* 4.0 4.2 - - - +
172A GLY* 1.3 76.8 - - - +
174A VAL* 1.3 81.4 + - - +
175A ILE* 3.6 25.5 - - + +
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A VAL* 4.1 9.9 - - + -
63A VAL 3.5 6.3 - - - +
64A LEU* 3.8 17.3 - - + -
138A GLY* 2.8 25.4 + - - +
156A ILE* 3.8 20.6 - - + -
173A HIS* 1.3 85.1 + - - +
175A ILE* 1.3 60.1 + - - +
176A GLU* 3.4 27.4 - - - +
177A GLY 4.3 1.6 - - - -
178A MET* 3.8 35.0 - - + +
181A VAL* 4.3 1.1 - - + -
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Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 4.1 16.4 - - + -
63A VAL* 2.8 26.8 + - + +
64A LEU 4.2 0.4 - - - -
65A GLU* 3.6 49.4 - - + +
173A HIS* 3.6 14.8 - - + -
174A VAL* 1.3 75.8 - - - +
176A GLU* 1.3 63.2 + - + +
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Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ARG* 4.6 13.7 - - - +
62A VAL* 3.6 0.5 - - - -
63A VAL* 2.9 50.1 + - + +
174A VAL* 3.4 10.2 - - - +
175A ILE* 1.3 84.3 - - + +
177A GLY* 1.3 66.6 + - - +
178A MET 3.6 1.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il